The use and misuse of FTIR spectroscopy in the determination of protein structure

Demystifying the tropics: FTIR characterization of pantropical woods and their α-cellulose extracts for past atmospheric 14C reconstructions

To ensure unbiased tree-ring radiocarbon (14C) results, traditional pretreatments carefully isolate wood cellulose from extractives using organic solvents, among other chemicals. The addition of solvents is laborious, time-consuming, and can increase the risk of carbon contamination. Tropical woods show a high diversity in wood-anatomical and extractive composition, but the necessity of organic-solvent extraction for the 14C dating of these diverse woods remains untested. We applied a chemical treatment that excludes the solvent step on the wood of 8 tropical tree species sampled in South-America and Africa, with different wood-anatomical and extractive properties. We analyzed the success of the extractive removal along with several steps of the α-cellulose extraction procedure using Fourier Transform Infrared (FTIR) spectroscopy and further confirmed the quality of 14C measurements after extraction. The α-cellulose extracts obtained here showed FTIR-spectra free of signals from various extractives and the 14C results on these samples showed reliable results. The chemical method evaluated reduces the technical complexity required to prepare α-cellulose samples for 14C dating, and therefore can bolster global atmospheric 14C applications, especially in the tropics.

Isolation and characterization of nettle (Urtica dioica L.) seed proteins: Conversion of underutilized by-products of the edible oil industry into food emulsifiers

This study aimed to upcycle a byproduct of the edible oil industry, cold-pressed nettle seed meal (CPNSM), into a plant-based emulsifier, thereby increasing the sustainability of the food system. The protein content of the nettle seed protein (NSP) powder was 48.3% with glutamic acid (16.6%), asparagine (10.7%), and arginine (9.7%) being the major amino acids. NSPs had a denaturation temperature of 66.6 °C and an isoelectric point of pH 4.3. They could be used as emulsifiers to form highly viscous coarse corn oil-in-water emulsions (10% oil, 4% NSP). Nevertheless, 10-fold diluted emulsions exhibited rapid creaming under different pH (2-9), salt (0-500 mM NaCl) and temperature (>40 °C) conditions, but they were relatively stable to aggregation. Our findings suggest that NSPs could be used as emulsifiers in highly viscous or gelled foods, like dressings, sauces, egg, cheese, or meat analogs.

Cell invasive amyloid assemblies from SARS-CoV-2 peptides can form multiple polymorphs with varying neurotoxicity

The neurological symptoms of COVID-19, often referred to as neuro-COVID include neurological pain, memory loss, cognitive and sensory disruption. These neurological symptoms can persist for months and are known as Post-Acute Sequalae of COVID-19 (PASC). The molecular origins of neuro-COVID, and how it contributes to PASC are unknown, however a growing body of research highlights that the self-assembly of protein fragments from SARS-CoV-2 into amyloid nanofibrils may play a causative role. Previously, we identified two fragments from the SARS-CoV-2 proteins, Open Reading Frame (ORF) 6 and ORF10, that self-assemble into neurotoxic amyloid assemblies. Here we further our understanding of the self-assembly mechanisms and nano-architectures formed by these fragments and their biological responses. By solubilising the peptides in a fluorinated solvent, we eliminate insoluble aggregates in the starting materials (seeds) that change the polymorphic landscape of the assemblies. The resultant assemblies are dominated by structures with higher free energies (e.g. ribbons and amorphous aggregates) that are less toxic to cultured neurons but do affect their mitochondrial respiration. We also show the first direct evidence of cellular uptake of viral amyloids. This work highlights the importance of understanding the polymorphic behaviour of amyloids and the correlation to neurotoxicity, particularly in the context of neuro-COVID and PASC.

Collagen-targeted protein nanomicelles for the imaging of non-alcoholic steatohepatitis

In vivo molecular imaging tools hold immense potential to drive transformative breakthroughs by enabling researchers to visualize cellular and molecular interactions in real-time and/or at high resolution. These advancements will facilitate a deeper understanding of fundamental biological processes and their dysregulation in disease states. Here, we develop and characterize a self-assembling protein nanomicelle called collagen type I binding - thermoresponsive assembled protein (Col1-TRAP) that binds tightly to type I collagen in vitro with nanomolar affinity. For ex vivo visualization, Col1-TRAP is labeled with a near-infrared fluorescent dye (NIR-Col1-TRAP). Both Col1-TRAP and NIR-Col1-TRAP display approximately a 3.8-fold greater binding to type I collagen compared to TRAP when measured by surface plasmon resonance (SPR). We present a proof-of-concept study using NIR-Col1-TRAP to detect fibrotic type I collagen deposition ex vivo in the livers of mice with non-alcoholic steatohepatitis (NASH). We show that NIR-Col1-TRAP demonstrates significantly decreased plasma recirculation time as well as increased liver accumulation in the NASH mice compared to mice without disease over 4 hours. As a result, NIR-Col1-TRAP shows potential as an imaging probe for NASH with in vivo targeting performance after injection in mice. STATEMENT OF SIGNIFICANCE: Direct molecular imaging of fibrosis in NASH patients enables the diagnosis and monitoring of disease progression with greater specificity and resolution than do elastography-based methods or blood tests. In addition, protein-based imaging probes are more advantageous than alternatives due to their biodegradability and scalable biosynthesis. With the aid of computational modeling, we have designed a self-assembled protein micelle that binds to fibrillar and monomeric collagen in vitro. After the protein was labeled with near-infrared fluorescent dye, we injected the compound into mice fed on a NASH diet. NIR-Col1-TRAP clears from the serum faster in these mice compared to control mice, and accumulates significantly more in fibrotic livers.This work advances the development of targeted protein probes for in vivo fibrosis imaging.

Simultaneous co-assembly of collagen and glycosaminoglycans to build a biomimetic extracellular matrix for bone regeneration

Glycosaminoglycans (GAGs), also known as shape modules, are considered junctions that help define the shape of collagen matrix and further promote mineralization during osteogenesis. Many attempts have been made to immobilize GAGs on assembled collagen to modify the latter's surface state. However, it remains unclear how GAGs spontaneously identify collagen molecules during fibrillogenesis in vivo. Understanding the relationship between GAGs and collagen from both the bone physiology and materials science perspectives is of fundamental interest. Here, we introduced hyaluronic acid (HA, a main member of GAGs) during collagen self-assembly, in a process called modification cooperating with self-assembly (MCS). The molecular docking and morphological studies revealed that HA can help define collagen monomer deposition and thus promote fibrillogenesis through steric hindrance or by directly forming hydrogen bonds. Meanwhile, HA acts as a templating chaperone (TC) to increase the local mineral concentration within intrafibrillar channels but does not initiate nucleation, thus improving the crystallinity of formed apatite. The scaffolds synthesized through MCS model significantly improved the physicochemical stability and mechanical strength of collagen-based scaffolds. The optimized scaffolds promoted in-situ osteogenesis by stimulating the osteogenic differentiation of bone mesenchymal stem cells, either in an osteogenic medium, or after implantation into critical calvarial defects. This study provides novel insights towards evolving engineering scaffolds from inert supports to functional substitutes.

IR-EcoSpectra: Exploring sustainable ex situ and in situ FTIR applications for green chemical and pharmaceutical analysis

In various industries, particularly in the chemical and pharmaceutical fields, Fourier transform infrared spectroscopy (FTIR) spectroscopy provides a unique capacity to detect and characterise complex chemicals while minimising environmental damage by minimal waste generation and reducing the need for extensive sample preparation or use of harmful reagents. This review showcases the versatility of ex situ and in situ FTIR applications for substance identification, analysis, and dynamic monitoring. Ex situ FTIR spectroscopy's accuracy in identifying impurities, monitoring crystallisation processes, and regulating medication release patterns improves product quality, safety, and efficacy. Furthermore, its quantification capabilities enable more effective drug development, dosage procedures, and quality control practices, all of which are consistent with green analytical principles. On the other hand, in situ FTIR spectroscopy appears to be a novel tool for the real-time investigation of molecular changes during reactions and processes, allowing for the monitoring of drug release kinetics, crystallisation dynamics, and surface contacts, as well as providing vital insights into material behaviour. The combination of ex situ FTIR precision and in situ FTIR dynamic capabilities gives a comprehensive analytical framework for developing green practices, quality control, and innovation in the chemical and pharmaceutical industries. This review presents the wide range of applications of ex situ and in situ FTIR spectroscopy in chemical, pharmaceutical and medical fields as an analytical green chemistry tool. However, further study is required to fully realise FTIR's potential and develop new applications that improve sustainability in these areas.

Vertically Grown Bioinspired Diphenylalanine Nanowire-Coated Fabric for Oil-Water Separation

Due to the pervasive use of oil for energy and other industrial applications, solutions to oil-water separation have received a great deal of attention lately to address the environmental damage of oil spills and groundwater contamination. However, many of these separation methods are materially expensive and environmentally hazardous, require elaborate fabrication, or rely on large amounts of energy to function. Herein, we provide an effective low-cost method for oil-water separation based on the hydrophobicity induced by self-assembled bioinspired diphenylalanine peptide nanowires grown on polyester fabric. This modified polyester fabric mesh exhibits parahydrophobicity and oleophilicity due to the hierarchical nano-to-microscale surface roughness. This mesh also achieves consistent high water separation efficiencies of over 99% and an ultrahigh oil flux of up to 26.7 ± 5 kLm-2·h-1. The growth of bioinspired peptide-based nanostructures on fabrics using facile technique and their application in oil-water separation presents the potential for using bioinspired materials for environmental remediation while minimizing environmental footprint.

Analysis of protein-protein and protein-membrane interactions by isotope-edited infrared spectroscopy

The objective of this work is to highlight the power of isotope-edited Fourier transform infrared (FTIR) spectroscopy in resolving important problems encountered in biochemistry, biophysics, and biomedical research, focusing on protein-protein and protein membrane interactions that play key roles in practically all life processes. An overview of the effects of isotope substitutions in (bio)molecules on spectral frequencies and intensities is given. Data are presented demonstrating how isotope-labeled proteins and/or lipids can be used to elucidate enzymatic mechanisms, the mode of membrane binding of peripheral proteins, regulation of membrane protein function, protein aggregation, and local and global structural changes in proteins during functional transitions. The use of polarized attenuated total reflection FTIR spectroscopy to identify the spatial orientation and the secondary structure of a membrane-bound interfacial enzyme and the mode of lipid hydrolysis is described. Methods of production of site-directed, segmental, and domain-specific labeling of proteins by the synthetic, semisynthetic, and recombinant strategies, including advanced protein engineering technologies such as nonsense suppression and frameshift quadruplet codons are overviewed.

Chirality and pH Influence the Self-Assembly of Antimicrobial Lipopeptides with Diverse Nanostructures

Chirality plays a crucial role in the self-assembly of biomolecules in nature. Peptides show chirality-dependent conformation and self-assembly. Lipidation of peptides occurs in vivo and has recently been exploited in designed conjugates to drive self-assembly and enhance bioactivity. Here, a library of pH-responsive homochiral and heterochiral lipidated tripeptides has been designed. The designed lipopeptides comprise homochiral C16-YKK or C16-WKK (where all the amino acids are l-isomers), and two heterochiral conjugates C16-Ykk and C16-Wkk (where the two lysines are d-isomers). The self-assembly of all the synthesized lipopeptides in aqueous solution was examined using a combination of spectroscopic methods along with cryogenic-transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS). Interestingly, it was observed that at acidic pH all the lipopeptides self-assemble into micelles, whereas at basic pH the homochiral lipopeptides self-assemble into nanofibers, whereas the heterochiral lipopeptides self-assemble into nanotapes and nanotubes. A pH switch was demonstrated using a thioflavin T fluorescence probe of β-sheet structure present in the extended structures at pH 8. We demonstrate that both chirality and pH in lipopeptides influence the self-assembly behavior of the model tripeptides, which also show promising bioactivity. Good cytocompatibility is observed in hemolytic assays and antimicrobial activity against both Gram-negative and Gram-positive bacteria is shown through the determination of minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) values and live/dead bacteria staining assay.

The Impact of Green Physical Crosslinking Methods on the Development of Sericin-Based Biohydrogels for Wound Healing

Silk sericin (SS)-based hydrogels show promise for wound healing due to their biocompatibility, moisture regulation, and cell proliferation properties. However, there is still a need to develop green crosslinking methods to obtain non-toxic, absorbent, and mechanically strong SS hydrogels. This study investigated the effects of three green crosslinking methods, annealing treatment (T), exposure to an absolute ethanol vapor atmosphere (V.E), and water vapor (V.A), on the physicochemical and mechanical properties of SS and poly (vinyl alcohol) (PVA) biohydrogels. X-ray diffraction and Fourier-transform infrared spectroscopy were used to determine chemical structures. Thermal properties and morphological changes were studied through thermogravimetric analysis and scanning electron microscopy, respectively. The water absorption capacity, mass loss, sericin release in phosphate-buffered saline (PBS), and compressive strength were also evaluated. The results showed that physical crosslinking methods induced different structural transitions in the biohydrogels, impacting their mechanical properties. In particular, V.A hydrogen presented the highest compressive strength at 80% deformation owing to its compact and porous structure with crystallization and bonding sites. Moreover, both the V.A and T hydrogels exhibited improved absorption capacity, stability, and slow SS release in PBS. These results demonstrate the potential of green physical crosslinking techniques for producing SS/PVA biomaterials for wound healing applications.

Efficient disinfection of combined sewer overflows by ultraviolet/peracetic acid through intracellular oxidation with preserving cell integrity

Combined sewer overflows (CSOs) introduce microbial contaminants into the receiving water bodies, thereby posing risks to public health. This study systematically investigated the disinfection performance and mechanisms of the combined process of ultraviolet and peracetic acid (UV/PAA) in CSOs with selecting Escherichia coli (E. coli) as a target microbial contaminant. The UV/PAA process exhibited superior performance in inactivating E. coli in simulated CSOs compared with UV, PAA, and UV/H2O2 processes. Increasing the PAA dosage greatly enhanced the disinfection efficiency, while turbidity and organic matter hindered the inactivation performance. Singlet oxygen (1O2), hydroxyl (•OH) and organic radicals (RO•) contributed to the inactivation of E. coli, with •OH and RO• playing the prominent role. Variations of intracellular reactive oxygen species, malondialdehyde, enzymes activities, DNA contents and biochemical compositions of E. coli cells suggested that UV/PAA primarily caused oxidative damage to intracellular molecules rather than the damage to the lipids of the cell membrane, therefore effectively limited the regrowth of E. coli. Additionally, the UV/PAA process displayed an outstanding performance in disinfecting actual raw CSOs, achieving a 2.90-log inactivation of total bacteria after reaction for 4 min. These results highlighted the practical applicability and effectiveness of the UV/PAA process in the disinfection of CSOs.

Supramolecular Motion Enables Chondrogenic Bioactivity of a Cyclic Peptide Mimetic of Transforming Growth Factor-β1

Transforming growth factor (TGF)-β1 is a multifunctional protein that is essential in many cellular processes that include fibrosis, inflammation, chondrogenesis, and cartilage repair. In particular, cartilage repair is important to avoid physical disability since this tissue does not have the inherent capacity to regenerate beyond full development. We report here on supramolecular coassemblies of two peptide amphiphile molecules, one containing a TGF-β1 mimetic peptide, and another which is one of two constitutional isomers lacking bioactivity. Using human articular chondrocytes, we investigated the bioactivity of the supramolecular copolymers of each isomer displaying either the previously reported linear form of the mimetic peptide or a novel cyclic analogue. Based on fluorescence depolarization and 1H NMR spin-lattice relaxation times, we found that coassemblies containing the cyclic compound and the most dynamic isomer exhibited the highest intracellular TGF-β1 signaling and gene expression of cartilage extracellular matrix components. We conclude that control of supramolecular motion is emerging as an important factor in the binding of synthetic molecules to receptors that can be tuned through chemical structure.

Key charged residues influence the amyloidogenic propensity of the helix-1 region of serum amyloid A

Increased plasma levels of serum amyloid A (SAA), an acute-phase protein that is secreted in response to inflammation, may lead to the accumulation of amyloid in various organs thereby obstructing their functions. Severe cases can lead to a systemic disorder called AA amyloidosis. Previous studies suggest that the N-terminal helix is the most amyloidogenic region of SAA. Moreover, computational studies implicated a significant role for Arg-1 and the residue-specific interactions formed during the fibrillization process. With a focus on the N-terminal region of helix-1, SAA1-13, mutational analysis was employed to interrogate the roles of the amino acid residues, Arg-1, Ser-5, Glu-9, and Asp-12. The truncated SAA1-13 fragment was systematically modified by substituting the key residues with alanine or uncharged but structurally similar amino acids. We monitored the changes in the amyloidogenic propensities, associated conformational markers, and morphology of the amyloids resulting from the mutation of SAA1-13. Mutating out Arg-1 resulted in much reduced aggregation propensity and a lack of detectable β-structures alluding to the importance of salt-bridge interactions involving Arg-1. Our data revealed that by systematically mutating the key amino acid residues, we can modulate the amyloidogenic propensity and alter the time-dependent conformational variation of the peptide. When the behaviors of each mutant peptide were analyzed, they provided evidence consistent with the aggregation pathway predicted by MD simulation studies. Here, we detail the important temporal molecular interactions formed by Arg-1 with Ser-5, Glu-9, and Asp-12 and discuss its mechanistic implications on the self-assembly of the helix-1 region of SAA.

Prediction of Protein Targets in Ovarian Cancer Using a Ru-Complex and Carbon Dot Drug Delivery Therapeutic Nanosystems: A Bioinformatics and µ-FTIR Spectroscopy Approach

We predicted the protein therapeutic targets specific to a Ru-based potential drug and its combination with pristine and N-doped carbon dot drug delivery systems, denoted as RuCN/CDs and RuCN/N-CDs. Synchrotron-based FTIR microspectroscopy (µFTIR) in addition to bioinformatics data on drug structures and protein sequences were applied to assess changes in the protein secondary structure of A2780 cancer cells. µFTIR revealed the moieties of the target proteins' secondary structure changes only after the treatment with RuCN and RuCN/N-CDs. A higher content of α-helices and a lower content of β-sheets appeared in A2780 cells after RuCN treatment. Treatment with RuCN/N-CDs caused a substantial increase in parallel β-sheet numbers, random coil content, and tyrosine residue numbers. The results obtained suggest that the mitochondrion-related proteins NDUFA1 and NDUFB5 are affected by RuCN either via overexpression or stabilisation of helical structures. RuCN/N-CDs either induce overexpression of the β-sheet-rich protein NDUFS1 and affect its random coil structure or interact and stabilise its structure via hydrogen bonding between -NH2 groups from N-CDs with protein C=O groups and -OH groups of serine, threonine, and tyrosine residues. The N-CD nanocarrier tunes this drug's action by directing it toward a specific protein target, changing this drug's coordination ability and inducing changes in the protein's secondary structures and function.

Engineering fibronectin-templated multi-component fibrillar extracellular matrices to modulate tissue-specific cell response

Cells assemble fibronectin, the major extracellular matrix (ECM) protein, into fibrillar matrices, which serve as 3D architectural scaffolds to provide, together with other ECM proteins tissue-specific environments. Although recent approaches enable to bioengineer 3D fibrillar fibronectin matrices in vitro, it remains elusive how fibronectin can be co-assembled with other ECM proteins into complex 3D fibrillar matrices that recapitulate tissue-specific compositions and cellular responses. Here, we introduce the engineering of fibrillar fibronectin-templated 3D matrices that can be complemented with other ECM proteins, including vitronectin, collagen, and laminin to resemble ECM architectures observed in vivo. For the co-assembly of different ECM proteins, we employed their innate fibrillogenic mechanisms including shear forces, pH-dependent electrostatic interactions, or specific binding domains. Through recapitulating various tissue-specific ECM compositions and morphologies, the large scale multi-composite 3D fibrillar ECM matrices can guide fibroblast adhesion, 3D fibroblast tissue formation, or tissue morphogenesis of epithelial cells. In other examples, we customize multi-composite 3D fibrillar matrices to support the growth of signal propagating neuronal networks and of human brain organoids. We envision that these 3D fibrillar ECM matrices can be tailored in scale and composition to modulate tissue-specific responses across various biological length scales and systems, and thus to advance manyfold studies of cell biological systems.

Specific Detection of Uropathogenic Escherichia coli via Fourier Transform Infrared Spectroscopy Using an Optical Biosensor

Urinary tract infections (UTIs) are caused mainly by uropathogenic Escherichia coli (UPEC), accounting for both uncomplicated (75%) and complicated (65%) UTIs. Detecting UPEC in a specific, rapid, and timely manner is essential for eradication, and optical biosensors may be useful tools for detecting UPEC. Recently, biosensors have been developed for the selective detection of antigen-antibody-specific interactions. In this study, a methodology based on the principle of an optical biosensor was developed to identify specific biomolecules, such as the PapG protein, which is located at the tip of P fimbriae and promotes the interaction of UPEC with the uroepithelium of the human kidney during a UTI. For biosensor construction, recombinant PapG protein was generated and polyclonal anti-PapG antibodies were obtained. The biosensor was fabricated in silicon supports because its surface and anchor biomolecules can be modified through its various properties. The fabrication process was carried out using self-assembled monolayers (SAMs) and an immobilized bioreceptor (anti-PapG) to detect the PapG protein. Each stage of biosensor development was evaluated by Fourier transform infrared (FTIR) spectroscopy. The infrared spectra showed bands corresponding to the C-H, C=O, and amide II bonds, revealing the presence of the PapG protein. Then, the spectra of the second derivative were obtained from 1600 to 1700 cm-1 to specifically determine the interactions that occur in the secondary structures between the biological recognition element (anti-PapG antibodies) and the analyte (PapG protein) complex. The analyzed secondary structure showed β-sheets and β-turns during the detection of the PapG protein. Our data suggest that the PapG protein can be detected through an optical biosensor and that the biosensor exhibited high specificity for the detection of UPEC strains. Furthermore, these studies provide initial support for the development of more specific biosensors that can be applied in the future for the detection of clinical UPEC samples associated with ITUs.

Nutritional Evaluation of Milk Thistle Meal as a Protein Feedstuff for Diets of Dairy Cattle

The objective of this work is to investigate the chemical and nutritional value of milk thistle meal (MTM) in order to improve it and to provide theoretical support for its application in dairy cattle production. MTM was assessed in comparison with seven conventional protein feed sources, namely, soybean meal (SBM), cottonseed meal (CS), canola meal (CN), palm kernel meal (PK), rice bran meal (RB), corn germ meal (CG), and sesame meal (SS). The chemical composition of these feedstuffs was assessed using wet chemical analysis, the Cornell Net Carbohydrate and Protein System was used to evaluate the carbohydrate and protein fractions, and the in situ nylon bag technique and the modified three-step in vitro method were used to assess the rumen degradation and intestinal digestibility. Additionally, Fourier transform infrared technology was used to determine the feedstuff protein spectral molecular structure and its amino acid profile was also assessed. The result showed that MTM acid detergent fiber, lignin, unavailable nitrogen, and non-degradable carbohydrate content were higher than those of the other feedstuffs. It had a 17% and 36% rumen effective degradation rate of neutral detergent fiber and dry matter, respectively, and had the lowest small intestinal rumen undegradable protein digestibility rate. It was low in leucine, histidine, arginine, and proline, but high in methionine. The total area of amide I and amide II in the protein secondary structure was similar to that of CN and CS, and the amide I and II ratio was not different from that of RB. To sum up, MTM has a poor carbohydrate composition and is high in fiber but, in comparison to most other protein feeds, has a higher crude protein rumen effective degradation rate, similar to that of SBM, and it is a good source of methionine, a limiting amino acid. Hence, its nutritional value can be further improved for application in dairy feeding through processes such as microbial or enzymatic fermentation.

Multimodal Imaging Using Raman Spectroscopy and FTIR in a Single Analytical Instrument with a Microscope (Infrared Raman Microscopy AIRsight, Shimadzu): Opportunities and Applications

Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy are powerful analytical techniques widely used separately in different fields of study. Integrating these two powerful spectroscopic techniques into one device represents a groundbreaking advance in multimodal imaging. This new combination which merges the molecular vibrational information from Raman spectroscopy with the ability of FTIR to study polar bonds, creates a unique and complete analytical tool. Through a detailed examination of the microscope's operation and case studies, this article illustrates how this integrated analytical instrument can provide more thorough and accurate analysis than traditional methods, potentially revolutionising analytical sample characterisation. This article aims to present the features and possible uses of a unified instrument merging FTIR and Raman spectroscopy for multimodal imaging. It particularly focuses on the technological progress and collaborative benefits of these two spectroscopic techniques within the microscope system. By emphasising this approach's unique benefits and improved analytical capabilities, the authors aim to illustrate its applicability in diverse scientific and industrial sectors.

Structure-Dependent Water Responsiveness of Protein Block Copolymers

Biological water-responsive (WR) materials are abundant in nature, and they are used as mechanical actuators for seed dispersal by many plants such as wheat awns and pinecones. WR biomaterials are of interest for applications as high-energy actuators, which can be useful in soft robotics or for capturing energy from natural water evaporation. Recent work on WR silk proteins has shown that β-sheet nanocrystalline domains with high stiffness correlate with the high WR actuation energy density, but the fundamental mechanisms to drive water responsiveness in proteins remain poorly understood. Here, we design, synthesize, and study protein block copolymers consisting of two α-helical domains derived from cartilage oligomeric matrix protein coiled-coil (C) flanking an elastin-like peptide domain (E), namely, CEC. We use these protein materials to create WR actuators with energy densities that outperform mammalian muscle. To elucidate the effect of structure on WR actuation, CEC was compared to a variant, CECL44A, in which a point mutation disrupts the α-helical structure of the C domain. Surprisingly, CECL44A outperformed CEC, showing higher energy density and less susceptibility to degradation after repeated cycling. We show that CECL44A exhibits a higher degree of intermolecular interactions and is stiffer than CEC at high relative humidity (RH), allowing for less energy dissipation during water responsiveness. These results suggest that strong intermolecular interactions and the resulting, relatively steady protein structure are important for water responsiveness.

Comparison of the self-assembly and cytocompatibility of conjugates of Fmoc (9-fluorenylmethoxycarbonyl) with hydrophobic, aromatic, or charged amino acids

The self-assembly in aqueous solution of three Fmoc-amino acids with hydrophobic (aliphatic or aromatic, alanine or phenylalanine) or hydrophilic cationic residues (arginine) is compared. The critical aggregation concentrations were obtained using intrinsic fluorescence or fluorescence probe measurements, and conformation was probed using circular dichroism spectroscopy. Self-assembled nanostructures were imaged using cryo-transmission electron microscopy and small-angle X-ray scattering (SAXS). Fmoc-Ala is found to form remarkable structures comprising extended fibril-like objects nucleating from spherical cores. In contrast, Fmoc-Arg self-assembles into plate-like crystals. Fmoc-Phe forms extended structures, in a mixture of straight and twisted fibrils coexisting with nanotapes. Spontaneous flow alignment of solutions of Fmoc-Phe assemblies is observed by SAXS. The cytocompatibility of the three Fmoc-amino acids was also compared via MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] mitochondrial activity assays. All three Fmoc-amino acids are cytocompatible with L929 fibroblasts at low concentration, and Fmoc-Arg shows cell viability up to comparatively high concentration (0.63 mM).

Propitious catalytic response of immobilized α-amylase from G. thermoleovorans in modified APTES-Fe3O4 NPs for industrial bio-processing

Challenges in enzyme and product recovery are currently intriguing in modern biotechnology. Coping enzyme stability, shelf life and efficiency, nanomaterials-based immobilization were epitomized of industrial practice. Herein, a α-amylase from Geobacillus thermoleovorans was purified and bound effectively on to a modified 3-Aminopropyltriethoxysilane (APTES)-Fe3O4 nanoparticle. It was revealed that the carrier-bound enzyme catalysis (pH 8 and 60 °C) was significant in contrast to the free enzyme (pH 7.5 and 55 °C). Furthermore, Zn2+ and Cu2+ were shown to cause inhibitory effects in both enzyme states. Unlike chloroform, toluene, benzene, and butanol, minimal effects were observed with ethanol, acetone, and hexane. The bound enzyme retained 27.4 % of its initial activity after being stored for 36 days. In addition, the reusability of the bound enzyme showed a gradual decline in activity after the first cycle; however, after 13 cycles, its residual activity at 53 % was observed. These data proved significant enough to use this enzyme for industrial starch and analogous substrate bio-processing.

In-situ observation of silk nanofibril assembly via graphene plasmonic infrared sensor

Silk nanofibrils (SNFs), the fundamental building blocks of silk fibers, endow them with exceptional properties. However, the intricate mechanism governing SNF assembly, a process involving both protein conformational transitions and protein molecule conjunctions, remains elusive. This lack of understanding has hindered the development of artificial silk spinning techniques. In this study, we address this challenge by employing a graphene plasmonic infrared sensor in conjunction with multi-scale molecular dynamics (MD). This unique approach allows us to probe the secondary structure of nanoscale assembly intermediates (0.8-6.2 nm) and their morphological evolution. It also provides insights into the dynamics of silk fibroin (SF) over extended molecular timeframes. Our novel findings reveal that amorphous SFs undergo a conformational transition towards β-sheet-rich oligomers on graphene. These oligomers then connect to evolve into SNFs. These insights provide a comprehensive picture of SNF assembly, paving the way for advancements in biomimetic silk spinning.

Coiled-Coil Protein Hydrogels Engineered with Minimized Fiber Diameters for Sustained Release of Doxorubicin in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) lacks expressed protein targets, making therapy development challenging. Hydrogels offer a promising new route in this regard by improving the chemotherapeutic efficacy through increased solubility and sustained release. Moreover, subcutaneous hydrogel administration reduces patient burden by requiring less therapy and shorter treatment times. We recently established the design principles for the supramolecular assembly of single-domain coiled-coils into hydrogels. Using a modified computational design algorithm, we designed Q8, a hydrogel with rapid assembly for faster therapeutic hydrogel preparation. Q8 encapsulates and releases doxorubicin (Dox), enabling localized sustained release via subcutaneous injection. Remarkably, a single subcutaneous injection of Dox-laden Q8 (Q8•Dox) significantly suppresses tumors within just 1 week. This work showcases the bottom-up engineering of a fully protein-based drug delivery vehicle for improved TBNC treatment via noninvasive localized therapy.

Self-assembled poloxamer-legumin/vicilin nanoparticles for the nanoencapsulation and controlled release of folic acid

Plant-based food proteins are a promising choice for the preparation of nanoparticles (NPs) due to their high digestibility, low cost, and ability to interact with various compounds and nutrients. Moreover, nanoencapsulation offers a potential solution for protecting nutrients during processing and enhancing their bioavailability. This study aimed to develop and evaluate nanoparticles (NPs) based on legumin/vicilin (LV) proteins extracted from fava beans, with the goal of encapsulating and delivering a model nutraceutical compound, folic acid (FA). Specifically, NPs were self-assembled from LV proteins extracted from commercially available frozen fava beans using a pH-coacervation method with poloxamer 188 (P188) and chemically cross-linked with glutaraldehyde. Microscopy and spectroscopy studies were carried out on the empty and FA-loaded NPs in order to evaluate the particle morphology, size, size distribution, composition, mechanism of formation, impact of FA loading and release behavior. In vitro studies with Caco-2 cells also confirmed that the empty and FA-loaded nanoparticles were non-toxic. Thus, the LV-NPs are good candidates as food additives for the delivery and stabilization of nutrients as well as in drug delivery for the controlled release of therapeutics.

Dried Porous Biomaterials from Mealworm Protein Gels: Proof of Concept and Impact of Drying Method on Structural Properties and Zinc Retention

Dried porous materials can be found in a wide range of applications. So far, they are mostly prepared from inorganic or indigestible raw materials. The aim of the presented study was to provide a proof of concept for (a) the suitability of mealworm protein gels to be turned into dried porous biomaterials by either a combination of solvent exchange and supercritical drying to obtain aerogels or by lyophilization to obtain lyophilized hydrogels and (b) the suitability of either drying method to retain trace elements such as zinc in the gels throughout the drying process. Hydrogels were prepared from mealworm protein, subsequently dried using either method, and characterized via FT-IR, BET volume, and high-resolution scanning electron microscopy. Retention of zinc was evaluated via energy-dispersive X-ray spectroscopy. Results showed that both drying methods were suitable for obtaining dried porous biomaterials and that the drying method mainly influenced the overall surface area and pore hydrophobicity but not the secondary structure of the proteins in the gels or their zinc content after drying. Therefore, a first proof of concept for utilizing mealworm protein hydrogels as a base for dried porous biomaterials was successful and elucidated the potential of these materials as future sustainable alternatives to more conventional dried porous materials.

Fabrication and characterisation of collagen/pullulan ultra-thin fibers by electrospinning

Collagen electrospun fibers are promising materials for food packaging and tissue engineering. The conventional electrospinning of collagen, however, is usually carried out by dissolving it in organic reagents, which are toxic. In this study, collagen/pullulan (COL/PUL) ultra-thin fibers were prepared by electrospinning using acetic acid as a solvent. Compared to the conventional preparation method, the proposed method is safe and does not produce toxic solvent residues. The introduction of PUL increased the degree of molecular entanglement in the solution, so the viscosity of the COL/PUL electrospun solution increased from 0.50 ± 0.01 Pa∙s to 4.40 ± 0.08 Pa∙s, and the electrical conductivity decreased from 1954.00 ± 1.00 mS/cm to 1372.33 ± 0.58 mS/cm. Scanning electron microscopy analysis confirmed that PUL improved the spinnability of COL, and smooth, defect-free COL/PUL ultra-thin fibers with diameters of 215.32 ± 40.56 nm and 240.97 ± 53.93 nm were successfully prepared at a viscosity of greater than 1.18 Pa∙s. As the proportion of PUL increased, intramolecular hydrogen bonds became the dominant interaction between COL and PUL. The intermolecular hydrogen bonding content decreased from 52.05 % to 36.45 %, and the intramolecular hydrogen bonding content increased from 46.11 % to 62.95 %. The COL was gradually unfolded, the content of α-helices decreased from 33.57 % to 25.91 % and the random coils increased from 34.22 % to 40.09 %. More than 36 % of the triple helix fraction of COL was retained by the COL/PUL ultra-thin fibers, whereas only 16 % of the triple helix fraction of COL was retained by the COL nanofibers prepared with 2.2.2-trifluoroethanol. These results could serve as a reference for the development of green food COL-based fibers.

Inverted Transflection Spectroscopy of Live Cells Using Metallic Grating on Elevated Nanopillars

Water absorption of mid-infrared (MIR) radiation severely limits the options for vibrational spectroscopy of the analytes-including live biological cells-that must be probed in aqueous environments. While internal reflection elements, such as attenuated total reflection prisms and metasurfaces, partially overcome this limitation, such devices have their own limitations: ATR prisms are difficult to integrate with multiwell cell culture workflows, while metasurfaces suffer from a limited spectral range and small penetration depth into analytes. In this work, we introduce an alternative live cell biosensing platform based on metallic nanogratings fabricated on top of elevated dielectric pillars. For the MIR wavelengths that are significantly longer than the grating period, reflection-based spectroscopy enables broadband sensing of the analytes inside the trenches separating the dielectric pillars. Because the depth of the analyte twice-traversed by the MIR light excludes the highly absorbing thick water layer above the grating, we refer to the technique as inverted transflection spectroscopy (ITS). The analytic power of ITS is established by measuring a wide range of protein concentrations in solution, with the limit of detection in the single-digit mg mL-1. The ability of ITS to interrogate live cells that naturally wrap themselves around the grating is used to characterize their adhesion kinetic.

An Amino Acid-Enabled Separator for Effective Stabilization of Li Anodes

Fundamentally suppressing Li dendrite growth is known to be critical for realizing the potential high energy density for Li-metal batteries (LMBs). Inspired by the ionic transport function of proteins, we previously discovered that utilizing natural proteins was able to stabilize the Li anode but have not demonstrated how a specific amino acid of the protein enabled the function. In this study, we decorate the separator with Leucine (Leu) amino acid assisted by poly(acrylic acid) (PAA) for effectively stabilizing the Li-metal anode, so as to dramatically improve the cycling performance of LMBs. The decorated separator improves electrolyte wettability and effectively suppresses Li dendrite growth. As a result, the amino acid-enabled separator prolongs the cycle life of the symmetrical Li|Li cells, exhibits higher Coulombic efficiency in the Li|Cu cells, and improves the cycling performance in LMBs with the LiFePO4 cathode. This work is an initial study on applying a specific amino acid of proteins to enhance the performance of batteries, providing a new strategy on guiding Li+ deposition, and laying an important foundation for functional separator design of high-energy-density batteries.

Whey protein isolate-resveratrol complex as a radical scavenging foaming ingredient with increased ultraviolet stability

Functional foaming food ingredients play a vital role in preparing healthcare foods, however, the weak foamability and low photostability of ingredients severely limit their further development. Herein, whey protein isolate-resveratrol complexes (WPI-RES) were fabricated to address these challenges. Multi-spectral analysis and molecular simulation results revealed the key driving forces of hydrogen bonding and hydrophobic interactions to promote the formation of WPI-RES complexes, leading to the enhanced foamability and emulsifying properties of WPI after binding with RES. Importantly, the robust radical scavenging activity of RES within WPI was maintained under UV light irradiation compared to that of free RES as identified by DPPH assay, which was presumably due to inhibited photoisomerization of RES after binding to WPI. This work provides a promising foaming ingredient with increased ultraviolet stability and radical scavenging activity, paves the way to develop stable health-promoting foaming food products.

Self-Assembly and Antimicrobial Activity of Lipopeptides Containing Lysine-Rich Tripeptides

The conformation and self-assembly of two pairs of model lipidated tripeptides in aqueous solution are probed using a combination of spectroscopic methods along with cryogenic-transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS). The palmitoylated lipopeptides comprise C16-YKK or C16-WKK (with two l-lysine residues) or their respective derivatives containing d-lysine (k), i.e., C16-Ykk and C16-Wkk. All four molecules self-assemble into spherical micelles which show structure factor effects in SAXS profiles due to intermicellar packing in aqueous solution. Consistent with micellar structures, the tripeptides in the coronas have a largely unordered conformation, as probed using spectroscopic methods. The molecules are found to have good cytocompatibility with fibroblasts at sufficiently low concentrations, although some loss of cell viability is noted at the highest concentrations examined (above the critical aggregation concentration of the lipopeptides, determined from fluorescence dye probe measurements). Preliminary tests also showed antimicrobial activity against both Gram-negative and Gram-positive bacteria.

Improved encapsulation effect and structural properties of whey protein isolate by dielectric barrier discharge cold plasma

The whey protein isolate (WPI) was modified by dielectric barrier discharge cold plasma (DBD) in order to improve its encapsulation efficiency of rutin. In this work, the effect of DBD treatment on structure and physicochemical properties of WPI and the interaction between DBD-treated WPI and rutin were investigated. The results showed that the structural change of WPI leaded to the exposure of internal hydrophobic groups, increasing the interaction site with rutin. The encapsulation efficiency of DBD-treated WPI (30 kV, 30 s) on rutin was improved by 12.42 % compared with control group. The results of multispectral analysis showed that static quenching occurred in the process of interaction between DBD-treated and rutin, hydrogen bond and van der Waals force were the main forces between them. Therefore, DBD treatment can be used as a method to improve the encapsulation efficiency of WPI on hydrophobic active substances.

Peptide Amphiphiles as Biodegradable Adjuvants for Efficient Retroviral Gene Delivery

Retroviral gene delivery is the key technique for in vitro and ex vivo gene therapy. However, inefficient virion-cell attachment resulting in low gene transduction efficacy remains a major challenge in clinical applications. Adjuvants for ex vivo therapy settings need to increase transduction efficiency while being easily removed or degraded post-transduction to prevent the risk of venous embolism after infusing the transduced cells back to the bloodstream of patients, yet no such peptide system have been reported thus far. In this study, peptide amphiphiles (PAs) with a hydrophobic fatty acid and a hydrophilic peptide moiety that reveal enhanced viral transduction efficiency are introduced. The PAs form β-sheet-rich fibrils that assemble into positively charged aggregates, promoting virus adhesion to the cell membrane. The block-type amphiphilic sequence arrangement in the PAs ensures efficient cell-virus interaction and biodegradability. Good biodegradability is observed for fibrils forming small aggregates and it is shown that via molecular dynamics simulations, the fibril-fibril interactions of PAs are governed by fibril surface hydrophobicity. These findings establish PAs as additives in retroviral gene transfer, rivalling commercially available transduction enhancers in efficiency and degradability with promising translational options in clinical gene therapy applications.

Fava bean (Vicia faba L.) protein concentrate added to beef burgers improves the bioaccessibility of some free essential amino acids after in vitro oral and gastrointestinal digestion

The influence of partial replacement of animal protein by plant-based ingredients on the protein digestibility of beef burgers was investigated. Beef burgers were supplemented with fava bean protein concentrate (FB) or a mixture of FB and flaxseed flour (FBFS), both processed by extrusion, at different levels: 0 (control), 10, 15, and 20 % (w/w). A pilot sensory analysis was conducted to select the percentage of flour inclusion for further assays: control, 10 % FB, and 10 % FBFS. Protein digestibility, amino acid profile, and protein secondary structure of these burgers after in vitro oral and gastrointestinal digestion were studied. In vitro boluses were prepared with the AM2 masticator, simulating normal mastication, and static in vitro digestion of boluses was performed according to the INFOGEST method. Inclusion of 10 % FB in beef burgers did not alter their flavour or tenderness compared to the control, whereas tenderness and juiciness scored slightly higher for the 10 % FBFS burgers compared to 15 % and 20 % FBFS ones. Poor lipid oxidative stability during storage was observed with 10 % FBFS burgers. Total protein content was significantly higher (p < 0.05) in 10 % FB burgers than in control burgers after in vitro oral digestion. Additionally, 10 % FB burgers presented higher amounts of free essential amino acids like isoleucine, leucine, phenylalanine, and valine at the end of digestion, as well as methionine, tyrosine, and histidine. Partial substitution of meat protein by 10 % FB improves the nutritional profile of beef burgers, without altering their sensory qualities.

Uncovering supramolecular chirality codes for the design of tunable biomaterials

In neurodegenerative diseases, polymorphism and supramolecular assembly of β-sheet amyloids are implicated in many different etiologies and may adopt either a left- or right-handed supramolecular chirality. Yet, the underlying principles of how sequence regulates supramolecular chirality remains unknown. Here, we characterize the sequence specificity of the central core of amyloid-β 42 and design derivatives which enable chirality inversion at biologically relevant temperatures. We further find that C-terminal modifications can tune the energy barrier of a left-to-right chiral inversion. Leveraging this design principle, we demonstrate how temperature-triggered chiral inversion of peptides hosting therapeutic payloads modulates the dosed release of an anticancer drug. These results suggest a generalizable approach for fine-tuning supramolecular chirality that can be applied in developing treatments to regulate amyloid morphology in neurodegeneration as well as in other disease states.

A novel bifunctional multilayered nanofibrous membrane combining polycaprolactone and poly (vinyl alcohol) enriched with platelet lysate for skin wound healing

Skin wound healing is a complex physiological process that involves various cell types, growth factors, cytokines, and other bioactive compounds. In this study, a novel dual-function multilayered nanofibrous membrane is developed for chronic wound application. The membrane is composed of five alternating layers of polycaprolactone (PCL) and poly (vinyl alcohol) (PVA) nanofibers (PCL-PVA) with a dual function: the PCL nanofibrous layers allow cell adhesion and growth, and the PVA layers enriched with incorporated platelet lysate (PCL-PVA + PL) serve as a drug delivery system for continuous release of bioactive compounds from PL into an aqueous environment. The material is produced using a needleless multi-jet electrospinning approach which can lead to homogeneous large-scale production. The bioactive PCL-PVA + PL membranes are cytocompatible and hemocompatible. A spatially compartmented co-culture of three cell types involved in wound healing - keratinocytes, fibroblasts and endothelial cells - is used for cytocompatibility studies. PCL-PVA + PL membranes enhance the proliferation of all cell types and increase the migration of both fibroblasts and endothelial cells. The membranes are also hemocompatible without any deleterious effect for thrombogenicity, hemolysis and coagulation. Thus, the beneficial effect of the PCL-PVA + PL membrane is demonstrated in vitro, making it a promising scaffold for the treatment of chronic wounds.

Endothelial leakiness elicited by amyloid protein aggregation

Alzheimer's disease (AD) is a major cause of dementia debilitating the global ageing population. Current understanding of the AD pathophysiology implicates the aggregation of amyloid beta (Aβ) as causative to neurodegeneration, with tauopathies, apolipoprotein E and neuroinflammation considered as other major culprits. Curiously, vascular endothelial barrier dysfunction is strongly associated with Aβ deposition and 80-90% AD subjects also experience cerebral amyloid angiopathy. Here we show amyloid protein-induced endothelial leakiness (APEL) in human microvascular endothelial monolayers as well as in mouse cerebral vasculature. Using signaling pathway assays and discrete molecular dynamics, we revealed that the angiopathy first arose from a disruption to vascular endothelial (VE)-cadherin junctions exposed to the nanoparticulates of Aβ oligomers and seeds, preceding the earlier implicated proinflammatory and pro-oxidative stressors to endothelial leakiness. These findings were analogous to nanomaterials-induced endothelial leakiness (NanoEL), a major phenomenon in nanomedicine depicting the paracellular transport of anionic inorganic nanoparticles in the vasculature. As APEL also occurred in vitro with the oligomers and seeds of alpha synuclein, this study proposes a paradigm for elucidating the vascular permeation, systemic spread, and cross-seeding of amyloid proteins that underlie the pathogeneses of AD and Parkinson's disease.

Modulating the properties of myofibrillar proteins-stabilized high internal phase emulsions using chitosan for enhanced 3D-printed foods

The 3D printability of myofibrillar proteins (MP)-based high internal phase emulsions (HIPEs) is a concern. This study investigated the influence of chitosan (CS) concentrations (0-1.5 wt%) on the physicochemical properties, microstructure, rheological properties, and stability of MP-based HIPEs. Results showed that the interaction between MP and CS efficiently modulated the formation of HIPEs by modifying interfacial tension and network structure. The addition of CS (≤ 0.9 wt%, especially at 0.6 wt%) acted as a spatial barrier, filling the network between droplets, which triggered electrostatic repulsion between CS and MP particles, enhancing MP's interfacial adsorption capacity. Consequently, droplet sizes decreased, emulsion stability increased, and HIPEs became more stable during freeze-thaw cycles, centrifugation, and heat treatment. The rheological analysis further demonstrated that the low energy storage modulus (G', 330.7 Pa) of MP-based HIPEs exhibited sagging and deformation during the self-supporting phase. However, adding CS (0.6 wt%) significantly increased the G' (1034 Pa) of MP-based HIPEs. Conversely, increasing viscosity and spatial resistance attributed to CS (> 0.9 wt%) noticeably caused larger droplet sizes, thereby diminishing the printability of MP-based HIPEs. These findings provide a promising strategy for developing high-performance and consumer-satisfaction 3D printing inks using MP-stabilized HIPEs.

Covalent Organic Frameworks for the Purification of Recombinant Enzymes and Heterogeneous Biocatalysis

Recombinant enzymes have gained prominence due to their diverse functionalities and specificity and are often a greener alternative in biocatalysis. This context makes purifying recombinant enzymes from host cells and other impurities crucial. The primary goal is to isolate the pure enzyme of interest and ensure its stability under ambient conditions. Covalent organic frameworks (COFs), renowned for their well-ordered structure and permeability, offer a promising approach for purifying histidine-tagged (His-tagged) enzymes. Furthermore, immobilizing enzymes within COFs represents a growing field in heterogeneous biocatalysis. In this study, we have developed a flow-based technology utilizing a nickel-infused covalent organic framework (Ni-TpBpy COF) to combine two distinct processes: the purification of His-tagged enzymes and the immobilization of enzymes simultaneously. Our work primarily focuses on the purification of three His-tagged enzymes β-glucosidase, cellobiohydrolase, and endoglucanase as well as two proteins with varying molecular weights, namely, green fluorescent protein (27 kDa) and BG Rho (88 kDa). We employed Ni-TpBpy as a column matrix to showcase the versatility of our system. Additionally, we successfully obtained a Ni-TpBpy COF immobilized with enzymes, which can serve as a heterogeneous catalyst for the hydrolysis of p-nitrophenyl-β-d-glucopyranoside and carboxymethylcellulose. These immobilized enzymes demonstrated catalytic activity comparable to that of their free counterparts, with the added advantages of recyclability and enhanced stability under ambient conditions for an extended period, ranging from 60 to 90 days. This contrasts with the free enzymes, which do not maintain their activity as effectively over time.

Enzymatic Preparation and Processing Properties of DPP-IV Inhibitory Peptides Derived from Wheat Gluten: Effects of Pretreatment Methods and Protease Types

The choice of appropriate proteases and pretreatment methods significantly influences the preparation of bioactive peptides. This study aimed to investigate the effects of different pretreatment methods on the hydrolytic performance of diverse proteases during the production of dipeptidyl peptidase-IV (DPP-IV) inhibitory peptides derived from wheat and their foaming and emulsion properties. Dry heating, aqueous heating, and ultrasound treatment were employed as pretreatments for the protein prior to the enzymatic hydrolysis of wheat gluten. FTIR analysis results indicated that all pretreatment methods altered the secondary structure of the protein; however, the effects of dry heating treatment on the secondary structure content were opposite to those of aqueous heating and ultrasound treatment. Nevertheless, all three methods enhanced the protein solubility and surface hydrophobicity. By using pretreated proteins as substrates, five different types of proteases were employed for DPP-IV inhibitory peptide production. The analysis of the DPP-IV inhibitory activity, degree of hydrolysis, and TCA-soluble peptide content revealed that the specific pretreatments had a promoting or inhibiting effect on DPP-IV inhibitory peptide production depending on the protease used. Furthermore, the pretreatment method and the selected type of protease collectively influenced the foaming and emulsifying properties of the prepared peptides.

Computational Prediction of Coiled-Coil Protein Gelation Dynamics and Structure

Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled-coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled-coil hydrogel design. Using Rosetta energy scores and Poisson-Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled-coil proteins while simultaneously exploring five new coiled-coil protein hydrogel sequences. Provided this library, we explore the impact of in silico energies on structure and gelation kinetics, where we also reveal a range of blue autofluorescence that enables hydrogel disassembly and recovery. As a result of this library, we identify the new coiled-coil hydrogel sequence, Q5, capable of gelation within 24 h at 4 °C, a more than 2-fold increase over that of our previous iteration Q2. The fast gelation time of Q5 enables the assessment of structural transition in real time using small-angle X-ray scattering (SAXS) that is correlated to coarse-grained and atomistic molecular dynamics simulations revealing the supramolecular assembling behavior of coiled-coils toward nanofiber assembly and gelation. This work represents the first system of hydrogels with predictable self-assembly, autofluorescent capability, and a molecular model of coiled-coil fiber formation.

What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments

Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically β-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-'α-helical' in proteins), KAM(α), ALA(α), DIC(α), EKF(α), IYI(pro-β-sheet or more generally, pro-extended), and VIV(β), and the reference α-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly showed that the pro-helical vs. pro-extended propensities start to emerge already at the level of tripeptides and can be fully developed at longer sequences. We postulate that certain short peptide sequences can be considered minimal "folding seeds". Admittedly, the inherent secondary structure propensity can be overruled by the large intramolecular interaction energies within the folded and compact protein structures. Still, the correlation of experimental and computational data presented herein suggests that the secondary structure propensity should be considered as one of the key factors that may lead to understanding the underlying physico-chemical principles of protein structure and folding from the first principles.

Chicken egg white precipitates induced by water dilution

Chicken egg whites (whole egg white, EW; thick egg white, TKEW; thin egg white, TNEW) become turbid and are accompanied by the formation of precipitates after being diluted with an equal mass of deionized water. The precipitates of TKEW induced by water dilution (Thick Egg White Precipitates, TKEWP) account for 14.47 % of TKEW total dry matter, much higher than that of thin egg white precipitates (TNEWP) (1.51 %) and whole egg white precipitates (EWP) (5.53 %). Quantitative proteomic analysis identified 27 differentially abundant proteins (p < 0.05) among EW, EWP, TNEWP, and TKEWP. Lysozyme was found to be a key protein in the formation of EW precipitates induced by water dilution, as its abundance was significantly higher in TNEWP and TKEWP. Mucin-5B (α-ovomucin) had the highest abundance in TKEWP, suggesting that its insolubility is one of the important factors contributing to the large formation of TKEWP. This paper systematically studies the formation, characteristics, and composition of egg white precipitation caused by water dilution, and puts forward a new understanding of the processing characteristics of egg white liquid, thus laying a theoretical foundation for further research methods to reduce egg white precipitation by water dilution.

Structural and Functional Insights into the Biomineralized Zeolite Imidazole Frameworks

Biomineralization is a natural process of mineral formation mediated by biomacromolecules, allowing access to hierarchical structures integrating biological, chemical, and material properties. In this contribution, we comprehensively investigate the biomineralization of zeolite imidazole frameworks (ZIFs) for one-step synthesis of an enzyme-MOF biocomposite, in terms of differential crystallization behaviors, fine microstructure of resultant ZIF biominerals, the enzyme's conformation evolution, and protective effect of ZIF mineral. We discover that the biomineralization ability is ZIF organic linker dependent and the biocatalytic function is highly related to the ZIF mineral species and their distinguishable topologies and defect structures. Importantly, a side-by-side analysis suggests that the protective effect of ZIF mineral toward the hosted enzyme is highly associated with the synergistic effect of size dimension and chemical microenvironment of the ZIF pores. This work provides important insight into the ZIF-dependent biomineralization behaviors and highlights the important role of the ZIF microstructure in its biocatalytic activity and durability, which has been underestimated previously.

Effects of Process Variables on the Physicochemical, Textural, and Structural Properties of an Isolated Pea Protein-Based High-Moisture Meat Analog

This study investigated the optimal extrusion conditions required to produce an isolated pea protein (IPP)-based meat analog. High-moisture extrusion cooking (HMEC) was performed. The effects of the moisture content (55 and 60%), barrel temperature (165 and 175 °C), and screw speed (150 and 200 rpm) on the physicochemical, textural, and structural properties of the high-moisture meat analog (HMMA) were determined. The results showed that the moisture content had a significant effect (p < 0.05) on the physicochemical and textural properties of the HMMA. A lower moisture content had significant impact (p < 0.05) on enhancing the texturization of the HMMA and the formation of fibrous structures, thereby increasing the texture profile analysis (TPA) and cutting strength of the HMMA. Protein denaturation during HMEC resulted in a lower protein solubility of the meat analog than the raw material. The content of β-sheets and β-turns in the meat analogs were higher than that in the raw material, while the content of random coils and α-helices is inversely proportional. The process variables had no significant (p > 0.05) effect on the secondary structures. In conclusion, the moisture content is the most important factor affecting the properties of HMMAs. The extrusion process variables for HMMAs are a moisture content of 55%, a barrel temperature of 175 °C, and a screw speed of 200 rpm.

Albumin from sera of rheumatoid arthritis patients share multiple biochemical, biophysical and immunological properties with in vitro generated glyco-nitro-oxidized-albumin

The purpose of the present study is to explore the effects of endogenous stressors on structure and function of rheumatoid arthritis (RA) patients' albumin. In contrast to glycated-albumin or nitro-oxidized-albumin, high titre antibodies against glyco-nitro-oxidized-albumin were found in the sera of RA patients. Also, compared to the other two modified forms of albumin, glyco-nitro-oxidized-albumin showed highest percent inhibition. Albumin isolated from RA patients' sera displayed hyperchromicity and quenching of tyrosine and tryptophan fluorescence. Fluorescence spectroscopy studies also revealed the presence of dityrosine and advanced glycation end products in RA patient's albumin. RA patients' albumin showed weaker binding with 1-anilinonaphthalene-8-sulfonic acid dye. Secondary structure alterations were demonstrated by circular dichroism and Fourier transform infrared spectroscopy. Biochemical investigations revealed substantial decline in the availability of free side chains of amino acid residues; increased carbonyls and decreased sulfhydryls in RA patients' albumin. The functional impairment in RA patients' albumin was revealed by their low binding with bilirubin and cobalt. Liquid chromatography mass spectrometry analysis revealed the presence of Nε-(carboxymethyl) lysine and 3-nitrotyrosine in RA patients' albumin. The amyloidogenic aggregation of RA patients' albumin was confirmed by Congo red absorption and thioflavin-T fluorescence assays. The morphology of the aggregates was visualized under scanning and transmission electron microscope. From the above findings, we inferred that endogenous stress in RA patients have modified albumin and produce structural/functional abnormalities. Also, the presence of anti-glyco-nitro-oxidized-albumin antibodies along with other clinical features may be used as biomarker for the diagnosis and assessment of treatment responses in RA patients.Communicated by Ramaswamy H. Sarma.

Predict the Gelling Properties of Alkali-Induced Egg White Gel Based on the Freshness of Duck Eggs

Preserved egg white (PEW) has excellent gelling properties but is susceptible to the freshness of raw eggs. In this study, the correlation between the comprehensive freshness index (CFI) of raw eggs and the gelling properties of alkali-induced egg white gel (EWG) was elucidated. Results showed that the CFI, established by a principal component analysis (PCA) and stepwise regression analysis (SRA) methods, can be used to predict the freshness of duck eggs under storage conditions of 25 °C and 4 °C. A correlation analysis demonstrated that the CFI showed a strong negative correlation with the hardness and chewiness of alkali-induced EWG and a strong positive correlation with resilience within 12 days of storage at 25 °C and 20 days at 4 °C (p < 0.01). It might be due to the decrease in α-helix and disulfide bonds, as well as the hydrophobic interactions showing a first decrease and then an increase within the tested days. This study can provide an important theoretical basis for preserved egg pickling.

Spectroscopic Investigation of Phosphorus Mineralization as Affected by the Calcite-Water Interfacial Chemistry

The mineralization and bioavailability of phytic acid, the predominant organic phosphorus (OP) species in many soils, have generally been rendered limited due to its interaction with soil minerals. In particularly calcareous and neutral to slightly alkaline soils, phytic acid is known to actively react with calcite, although how this interaction affects phytic acid mineralization is still unknown. This study, therefore, investigated the mechanisms regarding how the calcite-water interface influences phytic acid mineralization by phytase, at pHs 6 and 8 using in situ spectroscopic techniques including solution nuclear magnetic resonance and attenuated total reflection Fourier transform infrared spectroscopy. The findings indicated a pH-specific effect of the calcite-water interface. Inhibited phytase activity and thus impaired phytic acid mineralization were induced by calcite at pH 6, while the opposite effect was observed at pH 8. How the interaction between phytic acid and calcite and between phytase and calcite differed between the two pH values contributed to the pH-specific effect. The results demonstrate the importance of soil pH, enzyme-, and OP-clay mineral interactions in controlling the mineralization and transformation of OP and, consequently, the release of phosphate in soils. The findings can also provide implications for the management of calcite-rich and limed soils.

Ambidexterity and Left-Handedness Induced by Geminally Disubstituted γ Amino Acid Residues in Chiral 310 Helices

Chirality is an omnipresent feature in nature's architecture starting from simple molecules like amino acids to complex higher-order structures viz. proteins, DNA, and RNA. The L configuration of proteinogenic amino acids gives rise to right-handed helices. Ambidexterity is as rare in organisms as in molecules. There are only a few reports of ambidexterity in single-peptide molecules composed of either mixed L and D or achiral residues. Here, we report, for the first time, the ambidextrous and left-handed helical conformations in the chiral nonapeptides P1-P3 (Boc-LUVUγx,xULUV-OMe where U = Aib, x,x = 2,2/3,3/4,4), containing chiral L α amino acid residues, in addition to the usually observed right-handed helical conformation. The centrally located achiral γ residue, capable of adopting both left and right-handed helical conformations, induces its handedness on the neighboring chiral and achiral residues, leading to the observation of both left and right-handed helices in P2 and P3. The presence of a single water molecule proximal to the γ residue induces the reversal of helix handedness by forming distinct and stable water-mediated hydrogen bonds. This gives rise to ambidextrous helices as major conformers in P1 and P2. The absence of the observation of ambidexterity in P3 might be due to the inability of γ4,4 in the recruitment of a water molecule. Experiments (NMR, X-ray, and CD) and density functional theory (DFT) calculations suggest that the position of geminal disubstitution is crucial for determining the population of the amenable helical conformations (ambidextrous, left and right-handed) in these chiral peptides.

Inverted transflection spectroscopy of live cells using metallic grating on elevated nanopillars

Water absorption of mid-infrared (MIR) radiation severely limits the options for vibrational spectroscopy of the analytes - including live biological cells - that must be probed in aqueous environments. While internal reflection elements, such as attenuated total reflection prisms and metasurfaces, partially overcome this limitation, such devices have their own limitations: high cost, incompatibility with standard cell culture workflows, limited spectral range, and small penetration depth into the analyte. In this work, we introduce an alternative live cell biosensing platform based on metallic nanogratings fabricated atop elevated dielectric pillars. For the MIR wavelengths that are significantly longer than the grating period, reflection-based spectroscopy enables broadband sensing of the analytes inside the trenches separating the dielectric pillars. Because the depth of the analyte twice-traversed by the MIR light excludes the highly absorbing thick water layer above the grating, we refer to the technique as Inverted Transflection Spectroscopy (ITS). We demonstrate the analytic power of ITS by measuring protein concentrations in solution. The ability of ITS to interrogate live cells that naturally wrap themselves around the grating is also exploited to characterize their adhesion kinetics.

An adaptive modeling approach using spiking-augmentation method to improve chemometric model performance in bioprocess monitoring

Intensified and continuous processes require fast and robust methods and technologies to monitor product titer for faster analytical turnaround time, process monitoring, and process control. The current titer measurements are mostly offline chromatography-based methods which may take hours or even days to get the results back from the analytical labs. Thus, offline methods will not meet the requirement of real time titer measurements for continuous production and capture processes. FTIR and chemometric based multivariate modeling are promising tools for real time titer monitoring in clarified bulk (CB) harvests and perfusate lines. However, empirical models are known to be vulnerable to unseen variability, specifically a FTIR chemometric titer model trained on a given biological molecule and process conditions often fails to provide accurate predictions of titer in another molecule under different process conditions. In this study, we developed an adaptive modeling strategy: the model was initially built using a calibration set of available perfusate and CB samples and then updated by augmenting spiking samples of the new molecules to the calibration set to make the model robust against perfusate or CB harvest of the new molecule. This strategy substantially improved the model performance and significantly reduced the modeling effort for new molecules.